Stepwise Reaction Mechanism Research Articles

Investigation of reaction mechanisms of NO with CO on Pd1/MgO and Pd4/MgO catalysts

The stepwise and concerted reaction mechanisms of NO with CO on Pd1 atom and Pd4 cluster adsorbed on the MgO surface have been studied by using the DFT/B3LYP method with the embedded cluster model. The reaction barriers have been calculated by using the IMOMO method at the CCSD level. The results suggest that the rate-controlling step barrier of the NO dissociation on the supported Pd4 cluster for the stepwise reaction mechanism is about 57kcal/mol and lower by about 33kcal/mol than that on the single supported Pd atom. However, the concerted reaction pathways on the single supported Pd atom and four supported Pd atoms are energetically unfavorable with the barriers of about 98kcal/mol and 71kcal/mol, respectively. Compared to the concerted reaction mechanism, the stepwise reaction mechanism of NO+CO is a possible pathway of CO2 molecule formation on the supported Pd catalysts.

Glycine Peptide Bond Formation Catalyzed by Faujasite

The catalysis of peptide bond formation between two glycine molecules on H-FAU zeolite was computationally studied by the M08-HX density functional. Two reaction pathways, the concerted and the stepwise mechanism, starting from three differently adsorbed reactants, amino-bound, carboxyl-bound, and hydroxyl-bound, are studied. Adsorption energies, activation energies, and reaction energies, as well as the corresponding intrinsic rate constants were calculated. A comparison of the computed energetics of the various reaction paths for glycine indicates that the catalyzed reaction proceeds preferentially via the concerted reaction mechanism of the hydroxyl-bound configuration. This involves an eight-membered ring of the transition structure instead of the four-membered ring of the others. The step from the amino-bound configuration to glycylglycine is the rate-determining step of the concerted mechanism. It has an estimated activation energy of 51.2 kcal mol(-1). Although the catalytic reaction can also occur via the stepwise reaction mechanism, this path is not favored.

The formation and decomposition of firefly dioxetanone

Firefly bioluminescence has attracted great attention for many years. Some details of the mechanism underlying firefly bioluminescence remain elusive. In this study the formation and decomposition reactions of firefly dioxetanone (DO) have been investigated in the gas phase and in a solvent model with an appropriate dielectric constant. Firefly DO is identified as a key intermediate. The formation of DO involves a stepwise reaction mechanism: first the formation of the four-membered ring on the singlet potential surface but not on the triplet and then the departure of the PO 4 CH 3 2 - group. For the decomposition of DO, two possible reaction paths are proposed, one of which is reported for the first time.

Multireference Character of 1,3-Dipolar Cycloaddition of Ozone with Ethylene and Acrylonitrile

In the present study, the concerted and stepwise reaction mechanisms for 1,3-dipole cycloaddition of ozone with ethylene (1) and acrylonitrile (2) are investigated. The stationary points are optimized by using four hybrid R(U)DFT methods. A geometry optimization method based on an approximate spin projection (AP-opt method) is applied to eliminate a spin contamination from the broken-symmetry (BS) solution. The AP-opt method reveals that a diradical intermediate for the stepwise pathway is spurious due to the spin contamination. The revised reaction profile with no diradical intermediate supports the stereospecificity. On the basis of the experimental data, the RCCSD(T) method outperforms AP-UCCSD(T), AP-UBD(T), and MkMRCCSD(4e,4o) for the systems, indicating that the RCCSD(T) method can describe the diradical character of ozone within a framework of single reference wave function. The subsequent single point energy calculations show that the highly synchronous transition state is much more favorable than the asynchronous one for 1. In the case of 2, there is not much difference between two transition states because of its asymmetric structure and charge separations in the transition states.

Low-molecular weight hydrocarbons in vent fluids from the Main Endeavour Field, northern Juan de Fuca Ridge

Despite its location on sediment-free basalt, vent fluids from the Main Endeavour Field (MEF) contain chemical species that indicate fluids have interacted with sediments during circulation. We report on the distribution and isotopic abundances of organic compounds ( C 1– C 3 alkanes and alkenes, benzene and toluene) in fluids collected from the Main Endeavour Field (MEF) in July, 2000, to understand the processes that regulate their abundances and characterize fluid sources. Aqueous organic compounds are derived from the thermal alteration of sedimentary organic matter and subsequently undergo further oxidation reactions during fluid flow. Fluid:sediment mass ratios calculated using ΣNH 4 concentrations indicate that the sediments are distal to the MEF, resulting in a common reservoir of fluids for all of the vents. Following the generation from sediment alteration, aqueous organic compounds undergo secondary alteration reactions via a stepwise oxidation reaction mechanism. Alkane distributions and isotopic compositions indicate that organic compounds in MEF fluids have undergone a greater extent of alteration as compared to Middle Valley fluids, either due to differences in subsurface redox conditions or the residence time of fluids at subsurface conditions. The distributions of the aromatic compounds benzene and toluene are qualitatively consistent with the subsurface conditions indicated by equilibration of aqueous alkanes and alkanes. However, benzene and toluene do not achieve chemical equilibrium in the subsurface. Methane and CO 2 also do not equilibrate chemically or isotopically at reaction zone temperatures, a likely result of an insufficient reaction time after addition of CO 2 from magmatic sources during upflow. The organic geochemistry supports the assumption that the sediments with which MEF fluids interact has the same composition as sediments present in Middle Valley itself, and highlight differences in subsurface reaction zone conditions and fluid flow pathways at these two sites.

QM/MM Studies of Xanthine Oxidase: Variations of Cofactor, Substrate, and Active-Site Glu802

In continuation of our previous QM/MM study on the reductive half-reaction of wild-type xanthine oxidase, we consider the effects of variations in the cofactor, the substrate, and the active-site Glu802 residue on the reaction mechanism. Replacement of the sulfido ligand in the natural cofactor by an oxo ligand leads to a substantial increase in the computed barriers, consistent with the experimentally observed inactivity of this modified cofactor, whereas the selenido form is predicted to have lower barriers and hence higher activity. For the substrate 2-oxo-6-methylpurine, the calculated pathways for three different tautomers show great similarity to those found previously for xanthine, contrary to claims in the literature that the mechanisms for these two substrates are different. Compared with the wild-type enzyme, the conversion of xanthine to uric acid follows a somewhat different pathway in the Glu802 --> Gln mutant which exhibits a lower overall activity, in agreement with recently published kinetic data. The present results confirm the basic stepwise reaction mechanism and the orientation of the substrate that has been proposed in our previous QM/MM work on aldehyde oxidoreductase and xanthine oxidase.

New insights into the multi-step reaction pathway of the reductive half-reaction catalysed by aromatic amine dehydrogenase: a QM/MM study

Computational insight into the multi-step reaction cycle of aromatic amine dehydrogenase is presented, identifying the energy landscape and pathway for multiple proton transfers. This atomistic picture of the reaction sequence--including short-lived reaction intermediates and a stepwise reaction mechanism--bridges the gap between a small number of crystallographic snapshots.

Bimolecular hydrogen transfer in phenalene by a stepwise ene-like reaction mechanism

For the hydrogen transfer of phenalene, a bimolecular ene-like mechanism is proposed, which is preferable over the hypothesized unimolecular rearrangement in the literature. Unique SOMO-SOMO pi-bonding of phenalenyl reduces the barriers of pericyclic reactions significantly. Pi-bonding between radicals is being recognized as a novel type of bonding interaction. This paper adds to the use of this interaction by pointing out its effect on reaction barriers.

On the question of stepwise vs. concerted cleavage of RNA models promoted by a synthetic dinuclear Zn(ii) complex in methanol: implementation of a noncleavable phosphonate probe

To address the question of concerted versus a stepwise reaction mechanisms for the cyclization of the 2-hydroxypropyl aryl and alkyl RNA models (1a-k) promoted by dinuclear Zn(II) complex (4) at (s)spH 9.8 and 25 degrees C, the non-cleavable O-hydroxypropyl phenylphosphonate analogues 6a and 6b were subjected to the catalytic reaction in methanol. These phosphonates did not undergo isomerization in the study, the only observable methanolysis reaction being release of 1,2-propanediol and the formation of O-methyl phenylphosphonate. The observed first order rate constants for methanolysis promoted by 4 are k(obs)(6a) = (1.47 +/- 0.09) x 10(-4) s(-1) and k(obs)(6b) = (2.08 +/- 0.09) x 10(-6) s(-1), respectively. The rates of methanolysis of a series of O-aryl phenylphosphonates (8a-f) in the presence of increasing [4] were analyzed to provide binding constants, Kb, and the catalytic rate constant, kcat(max), for the unimolecular decomposition of the 8:4 Michaelis complex. A Brønsted plot of the log (k(cat)(max)) vs. sspKa(phenol) (acidity constant of the conjugate acid of the leaving group in methanol) was fitted to a linear regression of log kcat(max) = (-0.80 +/- 0.07)(s)spKa + (10.2 +/- 1.0) which includes the datum for 6a. The datum for 6b, which reacts approximately 70-fold slower, falls significantly below the linear correlation. The data provide additional evidence consistent with a concerted cyclization of RNA models 1a-k promoted by 4.

Thermal [2+3]‐Cycloadditions of trans‐1‐Methyl‐2,3‐diphenylaziridine with CS and CC Dipolarophiles: An Unexpected Course with Dimethyl Dicyanofumarate

AbstractThe thermal reaction of trans‐1‐methyl‐2,3‐diphenylaziridine (trans‐1a) with aromatic and cycloaliphatic thioketones 2 in boiling toluene yielded the corresponding cis‐2,4‐diphenyl‐1,3‐thiazolidines cis‐4 via conrotatory ring opening of trans‐1a and a concerted [2+3]‐cycloaddition of the intermediate (E,E)‐configured azomethine ylide 3a (Scheme 1). The analogous reaction of cis‐1a with dimethyl acetylenedicarboxylate (5) gave dimethyl trans‐2,5‐dihydro‐1‐methyl‐2,5‐diphenylpyrrole‐3,4‐dicarboxylate (trans‐6) in accord with orbital‐symmetry‐controlled reactions (Scheme 2). On the other hand, the reactions of cis‐1a and trans‐1a with dimethyl dicyanofumarate (7a), as well as that of cis‐1a and dimethyl dicyanomaleate (7b), led to mixtures of the same two stereoisomeric dimethyl 3,4‐dicyano‐1‐methyl‐2,5‐diphenylpyrrolidine‐3,4‐dicarboxylates 8a and 8b (Scheme 3). This result has to be explained via a stepwise reaction mechanism, in which the intermediate zwitterions 11a and 11b equilibrate (Scheme 6). In contrast, cis‐1,2,3‐triphenylaziridine (cis‐1b) and 7a gave only one stereoisomeric pyrrolidine‐3,4‐dicarboxylate 10, with the configuration expected on the basis of orbital‐symmetry control, i.e., via concerted reaction steps (Scheme 10). The configuration of 8a and 10, as well as that of a derivative of 8b, were established by X‐ray crystallography.

SOLVENT AND SUBSTITUENT EFFECTS ON THE INTRAMOLECULAR AMIDE HYDROLYSIS OF N-METHYLMALEAMIC ACID

Intramolecular amide hydrolysis of N-methylmaleamic acid is revisited at the B3LYP/6-311G(2df, p)//B3LYP/6-31G(d, p) + ZVPE level, including solvent effects at the CPCM-B3LYP/6-311G(2df, p)//Onsager-B3LYP/6-31G(d, p) + ZPVE level. The concerted reaction mechanism is energetically favorable over stepwise reaction mechanisms in both the gas phase and solution. The calculated reaction barriers are significantly lower in solution than in the gas phase. In addition, it is concluded that the substituents of the four N-methylmaleamic acid derivatives considered herein have a significant effect on the gas-phase reaction barriers but a smaller, or little, effect on the barriers in solution.

Stable Carbon Isotope Fractionation of 1,2-Dichloropropane during Dichloroelimination by Dehalococcoides Populations

The isotope fractionation of 1,2-dichloropropane (1,2-D) during dichloroelimination to propene by Dehalococcoides populations was explored in laboratory experiments in order to provide data for the characterization of the fate of 1,2-D in heterogeneous subsurface systems. Compound specific stable carbon isotope analysis (CSIA) was used to determine the bulk enrichment factors (epsilonbulk), reactive position specific enrichment factors (epsilonreactive), and apparent kinetic isotope effect (AKIE) values for 1,2-D dichloroelimination in two distinct Dehalococcoides-containing cultures. The epsilonbulk factors calculated in the two cultures were statistically identical, -10.8 +/- 0.9 and -11.3 +/- 0.8 per thousand, even though the cultures were derived from geographically distinct locations. AKIE values for 1,2-D dichloroelimination assuming stepwise and concerted reaction mechanisms were approximately 1.033 and 1.017, respectively. These values are within the range of previously reported values for dichloroelimination reactions and were equivalent to values reported for biotic 1,2-dichloroethane and abiotic 1,1,2,2,-tetrachloroethane and pentachloroethane dichloroelimination reactions.

Theoretical studies on the cycloaddition reaction of ethylene and formaldehyde

The potential energy surface of cycloaddition (H2CCH2 + H2CO) has been investigated by using the ab initio SCF MO method at extended (3–21G) level. All the critical points were optimized by energy gradient technique and characterized by computing the Hessian matrices with analytic method. The results of computations indicate that: (i) Stepwise reactions involving diradicaloid intermediates and transition states are more favorable than the concerted ones. (ii) There are two compatible stepwise reaction mechanism, one is to form C—C bond firstly, while the other is to form C—O bond at first. (iii) For the reverse reaction-thermolysis of oxetane, the cleavage of C—O bond is preferred over that of C—C bond.

Cr(CO)3‐Activated Diels–Alder Reaction on Single‐Wall Carbon Nanotubes: A DFT Investigation

Breaking barriers: In agreement with experimental evidence, it was found by means of high-level DFT calculations that the Cr(CO)(3) metal fragment considerably reduces the reaction energy barrier-for both the concerted and stepwise reaction mechanisms (see graphic)-of the Diels-Alder reaction of butadiene on (5,5) carbon nanotubes.The reaction mechanism and the effect of Cr(CO)(3) on the Diels-Alder reaction of butadiene on (5,5) carbon nanotube sidewalls have been investigated by high-level DFT calculations. We investigated both concerted and stepwise reaction pathways on closed-shell and open-shell potential-energy surfaces. In agreement with recent experimental evidence, we found the Cr(CO)(3) metal fragment to considerably reduce the reaction energy barrier, both for the concerted and stepwise reaction mechanisms. The latter mechanism, previously found to be higher in energy with traditional substrates, appears to compete with the concerted mechanism on the carbon nanotube sidewalls. An analysis of the frontier molecular orbitals on the pristine and Cr(CO)(3)-complexed carbon nanotubes allowed us to identify the reason for this inverted reactivity pattern and the role of the transition metal on the addition of the diene.

The potential energy surface of the triazadiphosphole formation

The formal GaCl3-assisted [3+2] cycloaddition of two (Me3Si)2N–N(SiMe3)–PCl2 molecules resulting in the formation of a triazadiphosphole has been studied by means of B3LYP/6-31G(d,p) computations. These calculations revealed a stepwise reaction mechanism starting from the disguised 1,3-dipole and dipolarophile (Me3Si)2N–N(SiMe3)–PCl2. Comparison of the potential energy surface for the formation of a triazadiphosphole in the presence and without a Lewis acid indicate, that addition of a Lewis acid such as GaCl3 decreases the activation barriers to Me3Si–Cl elimination, in accord with experiment.

Base-Mediated Reaction of Hydrazones and Nitroolefins with a Reversed Regioselectivity: A Novel Synthesis of 1,3,4-Trisubstituted Pyrazoles

A regioselective synthesis of 1,3,4-tri- or 1,3,4,5-tetrasubstituted pyrazoles by the reaction of hydrazones with nitroolefins is described. Mediated with strong bases such as t-BuOK, the reaction exhibits a reversed, exclusive 1,3,4-regioselectivity. Subsequent quenching with strong acids such as TFA is essential to achieve good yields. A plausible stepwise cycloaddition reaction mechanism is proposed.

Structure and Reaction Mechanism of Alkylation of Phenol with Methanol over H-FAU Zeolite: An ONIOM Study

The competitive methylation of phenol with methanol over nanoporous faujasite zeolite was studied within the framework of our-own-N-layered-integrated molecular orbital + molecular mechanics (ONIOM) approach with two proposed reaction pathways: stepwise and concerted mechanisms. The results obtained by the two-layer ONIOM(B3LYP/6-31G(d,p):UFF) scheme elucidate that the methylation preferentially takes place via a single-step concerted mechanism rather than by the stepwise mechanism. The reactivity difference between the O- and C-methylation became more obvious in the concerted mechanism where the O-methylation proceeded faster than the C-methylation. The activation energies of the O- and C-methylation were estimated to be 14.9 and 19.2 kcal/mol, respectively, comparing well with the available experimental data of phenol methylation on acidic zeolites. In the stepwise reaction mechanism, the formation of the surface methoxide species (activation energy of 39.6 kcal/mol) was the rate-determining step, whil...

A directly-dissociative stepwise reaction mechanism for gas-phase peroxyacetic acid

The dissociation of peroxyacetic acid (PAA, CH 3C(O)OOH) was studied by UV laser photolysis in the gas phase under collision-free conditions. Three pathways are proposed for PAA dissociation that ultimately produce CH 3 + CO 2 + OH. Two pathways are stepwise with sequential bond dissociation and the other pathway is concerted with simultaneous fission of the same bonds. The laser-induced fluorescence (LIF) spectrum of OH was analyzed after 266 and 240 nm photolysis of PAA. OH is produced in the 2Π ground electronic state with no vibrational energy ( v ″ = 0 ) and rotational distributions that peak at N″ ≈ 3–4 and extend to N″ = 11 at both photolysis wavelengths. Spin-orbit population ratios of the ground electronic state were slightly above unity for both studies. The average OH Λ-doublet ratio was 1.07 ± 0.14 after 266 nm photolysis, which indicates that OH is produced by torsional forces. At 240 nm PAA photolysis, the Λ-doublet ratio increased from unity at N″ = 4 to a statistical value of ∼2 at N″ = 11. Average OH translational energies determined from Doppler profiles were 34 ± 2 and 43 ± 2 kcal mol −1 at 266 and 240 nm photolysis, respectively. The average speed of OH is used to determine the total translational energy of products for the proposed stepwise and concerted pathways. The calculated total translational energies are compared to thermochemical available energy calculations for each pathway to determine the viability of the reactions. Experimental results indicate that dissociation occurs from an excited state, so a comparison of 266 and 240 nm photolysis data is made to discover the direct versus indirect nature of the mechanism. The UV spectra of PAA, acetic acid, hydrogen peroxide, and methylhydroperoxide are reviewed in light of the results. This study concludes that PAA photolysis occurs through initial stepwise O O bond dissociation by a directly-dissociative mechanism from a highly-repulsive electronic state like the hydroperoxides and an indirect mechanism from an exit channel barrier similar to acetic acid is not accessed at these wavelengths.

Origin of Diastereoselectivity in the Synthesis of Chiral Bicyclic Lactams: π-Facial Selective Attack of Singlet Oxygen Induced by Hindered Internal Rotation

Previously reported experimental results indicate that photooxygenation of homochiral N-(hydroxyalkyl)-2-methylpyrroles with singlet oxygen yields trans-rather than cis-bicyclic lactams as the major product. In this study, the origin of selectivity in this reaction has been investigated with computational methods. Relative stabilities of homochiral N-(hydroxyalkyl)-2-methylpyrrole conformers and their effect on pi-facial selectivity of 1O2 were extensively studied. Stepwise and concerted reaction mechanisms, starting from the endoperoxide intermediates, were proposed and modeled in vacuum using the UB3LYP method with the 6-31+G** basis set. Solvent calculations were carried out in CH2Cl2, by means of the integral equation formalism-polarizable continuum model (IEF-PCM) at the UB3LYP/6-31+G** level of theory. Free energies of activation leading to both diastereomers were analyzed in an effort to explain the stereoselectivity and product distribution. Steric interactions among the pyrrole substituents were shown to lead to a rotational barrier higher than 10 kcal/mol. Hence, hindered internal rotation is suggested to cause one pyrrole conformer to be substantially overpopulated. This in turn has a major effect on pi-facial selectivity of 1O2, thereby favoring one endoperoxide over the other and leading to the diastereoselective synthesis of trans-pyrrolooxazolones. The importance of hindered internal rotors, for an accurate calculation of the frequency factors of a chemical reaction, has already been mentioned in the literature many times; however, in this work hindered internal rotors also seem to dictate the diastereoselective outcome of the reaction.

Theoretical Study of the Reaction Mechanisms Involved in the Thermal Intramolecular Reactions of 1,6-Fullerenynes

Substitution of a H atom by an alkyl group on the terminal carbon of the alkyne moiety of 1,6-fullerenynes has a strong impact on the products of the reaction undergone by this species after thermal treatment. While the reaction of 1,6-fullerenynes bearing an unsubstituted alkyne moiety results in the cycloaddition of the alkyne group to the fullerene double bond leading to cyclobutene-fused derivatives, the presence of an alkyl substituent leads to the formation of allenes. In the present work, we have performed an exhaustive theoretical analysis of all possible reaction mechanisms leading to cyclobutene-fused derivatives and allenes to offer an explanation of the reactivity differences observed. The results obtained show that formation of cyclobutene-fused derivatives occurs through a stepwise diradical reaction mechanism, while allene formation proceeds through a concerted way involving an uncommon intramolecular ene process. For the 1,6-fullerenynes bearing a substituted alkyne, the ene reaction path leading to allenes has an energy barrier somewhat lower than the stepwise diradical mechanism for the cyclobutene-fused derivative formation, thus explaining the outcome of the reaction.